Lab Matters Fall 2023 | Page 99

APHL 2023 POSTER ABSTRACTS

Development of Real Time PCR Assays for Detecting Tick-borne Pathogens in Support of a Statewide Tick Surveillance Program

J . Occi , A . Preidel , C . Bilyeu , M . Ali , D . Woell ; New Jersey Department of Health Public Health and Environmental Laboratories

According to the US Centers for Disease Control and Prevention ( CDC ), New Jersey has tallied ~ 10 % of the country ’ s case load of tick-borne disease ( TBD ) cases for the last 30 years . In 2019 there were 48,494 cases of five different TBD * recorded in the US by the CDC , while the New Jersey Department of Health ( NJDOH ) recorded 4,319 cases – again 10 % of the country ’ s burden of TBD . To address this public health problem , in 2021 , NJDOH initiated a pilot tick surveillance program with funding from the CDC . The objectives were to : ( 1 ) enlist the expertise of the NJ county mosquito control agencies for tick surveillance , ( 2 ) training additional staff to supplement tick collections throughout the state and ( 3 ) develop assays at the state health lab for testing ticks for various pathogens . In NJ there are five species of tick that have the potential to transmit pathogens . They are : the lone star tick ( Amblyomma americanum ), the newly discovered Gulf Coast tick ( Amblyomma maculatum ), the American dog tick ( Dermacentor variabilis ), the Asian longhorned tick ( Heamaphysalis longicornis ) and the blacklegged tick ( Ixodes scapularis ). Each species of tick transmits different pathogens . Therefor we had to develop RT-PCR assays that would detect a pathogen or pathogens from each tick species . Here we describe the development of our real time polymerase chain reaction ( RT- PCR ) assays in support of a state-wide tick surveillance program .

* Lyme disease , Powassan virus infection , Ehrlichiosis , Babesiosis , Anaplasmosis and Spotted fever rickettsiosis .

Presenter : Aaron Preidel , aaron . preidel @ doh . nj . gov

Distribution of Carbapenem-Resistance Mechanisms among Enterobacterales , Pseudomonas aeruginosa , and Acinetobacter baumannii in Texas , 2017-2022

R . Tuladhar , K . Abella , C . Wang , C . Schroeder , D . Gehlbach ; Texas Department of State Health Services

Introduction : Antimicrobial resistance genes , such as carbapenemase , can be located on mobile genetic elements , making for easy transfer between bacteria . Carbapenemases are grouped into three classes : class A ( e . g ., blaKPC ), class B ( e . g ., blaIMP , blaNDM , blaVIM ), and class D ( e . g ., blaOXA ). As a member of the CDC Antimicrobial Resistance Lab Network ( ARLN ) since 2017 , the Texas Department of State Health Services ( DSHS ) has performed antimicrobial resistance ( AR ) testing for carbapenemresistant Enterobacterales ( CRE ), carbapenem-resistant Pseudomonas aeruginosa ( CRPA ), and carbapenem-resistant Acinetobacter baumanii ( CRAB ). Here , we describe carbapenemase gene frequency and distribution in the eleven Texas public health regions from 2017 to 2022 in order to build robust public health measures . Results : Using RT-PCR assays , the DSHS Laboratory tested 4,924 CRE ; 2,433 CRPA ; and 2,308 CRAB specimens . Specifically , the CRE specimens harbored class A ( 24.9 %), class B ( 4.6 %), and class D ( 1.3 %). We detected class A ( 1.1 %) and class B ( 8.9 %), but no class D ( 0 %), in the CRPA specimens . Finally , the CRAB specimens were positive for class B ( 1.1 %) and class D ( 67.4 %), but not class A ( 0 %). Interestingly , 0.36 % of specimens were positive for dual resistance mechanisms . As expected , the frequency of each class , and subclasses , varied by public health regions . Public health region 10 , which includes El Paso , had the highest frequency of class A . Depending on the subclass , regions 1 ( blaVIM ), 7 ( blaIMP ), and 10 ( blaNDM ) have the highest frequencies of class B . These include major cities such as Lubbock , Austin , and El Paso , respectively . Likewise , the highest frequencies of class D depended on the subclass also . These included public health regions 3 , 5 , 10 , and 11 for subclasses blaOXA-24 / 40-like , blaOXA-23-like , blaOXA-48-like , and blaOXA-58-like , respectively . Of note , subclass blaOXA-58-like was only detected in region 11 . Conclusion : Based on the samples collected in Texas between 2017 and 2022 , there was a considerable geographic distribution in carbapenem resistance mechanisms . The detection of dual resistance mechanisms against carbapenem is of great concern for treatment and prevention of infection . Understanding the frequency distribution of these mechanisms helps with the development of public health containment strategies . Further , these data have contributed substantially towards detecting AR organisms .

Presenter : Deanne Gehlbach , deanne . gehlbach @ dshs . texas . gov

Dynamic Molecular Surveillance of SARS-CoV-2 at the Regional Innovative Public Health Laboratory in Chicago , IL

H . J . Barbian 1 , K . English 2 , S . Bobrovska 1 , M . Fiorillo 2 , S . Green 1 , M . Hayden 1 , R . Teran 2 , Isaac Ghinai 2 ; 1 Rush University Medical Center ,

2

Chicago Department of Public Health

The Regional Innovative Public Health Laboratory ( RIPHL ) is a public-academic partnership between Chicago Department of Public Health ( CDPH ) and Rush University . It was established in March 2021 to serve as the molecular epidemiology laboratory for CDPH , providing flexible molecular detection , characterization and genomic surveillance of pathogens of public health importance with the goal of timely and actionable data for public health response . Between April 3 , 2021 and December 31 , 2022 , RIPHL received 11,557 SARS-CoV-2-positive remnant clinical respiratory specimens from 15 acute care hospitals in Chicago for molecular characterization . Of these , 8,886 ( 77 %) specimens were successfully sequenced and yielded lineage assignments . Across the study period , RIPHL sequenced 3 % of all incident SARS-CoV-2 infections reported to CDPH and accounted for 62 % of Chicago SARS-CoV-2 sequences in GISAID . Demographically , individuals who provided specimens for sequencing were broadly representative of all SARS-CoV-2 infections reported to CDPH in terms of sex , age , race / ethnicity and ZIP code of residence . RIPHL has altered molecular methods in response to public health needs . When Omicron BA . 1 was rapidly emerging , RIPHL developed and implemented a genotyping PCR to provide lineage proportion estimates at much faster turnaround compared to whole genome sequencing ( WGS ). TaqMan SARS-CoV-2 Mutation Panel Assays ( ThermoFisher ) targeting mutations K417N and L452R were used to distinguish BA . 1 from the background of Delta variant . Genotyping PCR was able to call lineage in samples with low viral concentration more successfully than WGS , resulting in 1,657 ( 90.4 %) lineage calls from genotyping PCR compared to 1,560 ( 85.1 %) for WGS . Of 1,541 samples with both WGS and genoptying PCR data available , 1,539 ( 99.9 %) concordant . Since late 2021 , Chicago has experienced waves of successive Omicron sublineages . The relative speed with which sublineages gained dominance was used as a proxy for the level of public health concern posed by particular sublineages . Logistic growth rates of emerging sublineages were calculated weekly : low risk